A first step towards determining the relationship between RNA cytidine modifications and RNA processing at a transcriptome-wide level involves the generation of appropriate tools. This project was initiated in FY2015 and we have made substantial progress towards establishing protocols for reliable immunoprecipitation of modified RNAs from diverse cellular pools. In addition, we have optimized procedures for high-efficiency bisulfite conversion of RNA through the incorporation of variably methylated spike-in controls. We are now at a stage where we are ready to harvest validated materials from several cellular pools for an initial round of high-throughput sequencing. Based on the data quality and preliminary results, we will determine the appropriate next steps.